The authors investigated orbital bone development in congenital microphthalmia (CM) using a three-dimensional finite element analysis model, after the orbital dimension deficiency was improved with a self-inflating hydrogel expander implant. Data of a 2-year-old male CM patient were examined. The orbital structure, eyeball, eye muscles, and self-inflating hydrogel expander were constructed according to computed tomography examination data. The effects of self-expanding spherical hydrogel at various locations in the muscle cone on orbital bone development were examined using 3-mL self-expanding expanders placed at shallow (model 1: 2 mm depth) and deep (model 2: 8 mm depth) muscle cone positions. This model simulated the hydrogel expansion process; the orbital bone biomechanics and radial displacement nephograms were obtained when the hydrogel volume increased 3, 5, 7, and 9 times and analyzed. The orbital bone biomechanics were concentrated at the medial orbital wall center, gradually spreading to the whole orbital wall. Biomechanics and radial displacement of the inferior temporal and lateral distal orbital wall region were the most significant, and were more significant in model 1 than in model 2. Finite element analysis is suitable for the biomechanical analysis of orbital development in CM. The shallow position inside CM patients' muscle cone is the optimal site for hydrogel implantation.